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. 2022 Jan 29;399(10323):437-446.
doi: 10.1016/S0140-6736(22)00017-4. Epub 2022 Jan 19.

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

Nicole Wolter  1 , Waasila Jassat  2 , Sibongile Walaza  3 , Richard Welch  2 , Harry Moultrie  4 , Michelle Groome  2 , Daniel Gyamfi Amoako  5 , Josie Everatt  6 , Jinal N Bhiman  7 , Cathrine Scheepers  7 , Naume Tebeila  6 , Nicola Chiwandire  6 , Mignon du Plessis  8 , Nevashan Govender  2 , Arshad Ismail  9 , Allison Glass  10 , Koleka Mlisana  11 , Wendy Stevens  12 , Florette K Treurnicht  12 , Zinhle Makatini  12 , Nei-Yuan Hsiao  13 , Raveen Parboosing  14 , Jeannette Wadula  15 , Hannah Hussey  16 , Mary-Ann Davies  16 , Andrew Boulle  16 , Anne von Gottberg  8 , Cheryl Cohen  17
Affiliations

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study

Nicole Wolter et al. Lancet. .

Abstract

Background: The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.

Methods: We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021.

Findings: From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity.

Interpretation: Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity.

Funding: The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.

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Conflict of interest statement

Declaration of interests CC has received grant support from the South African Medical Research Council, the UK Foreign, Commonwealth and Development Office, the Wellcome Trust, the US Centers for Disease Control and Prevention, and Sanofi Pasteur. NW and MdP have received grant support from Sanofi Pasteur and the Bill & Melinda Gates Foundation. AvG has received grant support from Sanofi Pasteur, the US Centers for Disease Control and Prevention, the South African Medical Research Council, the Bill & Melinda Gates Foundation, WHO, the Fleming Fund, and the Wellcome Trust. RW declares personal shareholding in Adcock Ingram Holdings, Dischem Pharmacies, Discovery, Netcare, and Aspen Pharmacare Holdings. WS has received grant support from the South African Medical Research Council, with funds received from the Department of Science and Innovation, and the Bill & Melinda Gates Foundation. All other authors declare no competing interests.

Figures

Figure 1
Figure 1
Number of COVID-19 cases detected and proportion of SGTF infections in South Africa by week Diagnosis for the proportion of SGTF infections was by the TaqPath PCR assay. Week 39 represents Oct 1, 2021, and week 48 represents Dec 4, 2021. DATCOV-Gen linked real-time SARS-CoV-2 test and genome data to detailed epidemiological and clinical data on hospitalised cases. SGTF=S gene target failure.
Figure 2
Figure 2
Number of SARS-CoV-2 delta variant and SGTF samples among hospitalised patients with COVID-19 and a known outcome in South Africa by epidemiological week and variant type Week 13 represents April 1, 2021, and week 49 represents Dec 6, 2021. DATCOV-Gen linked real-time SARS-CoV-2 test and genome data to detailed epidemiological and clinical data on hospitalised cases. SGTF=S gene target failure.
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References

    1. Viana R, Moyo S, Amoako DG, et al. Rapid epidemic expansion of the SARS-CoV-2 omicron variant in southern Africa. Nature. 2022 doi: 10.1038/d41586-021-03832-5. published online Jan 7. - DOI - PMC - PubMed
    1. National Institute for Communicable Diseases COVID-19 weekly epidemiology brief. South Africa. Week 48 2021. 2021. https://www.nicd.ac.za/wp-content/uploads/2021/12/COVID-19-Weekly-Epidem...
    1. WHO Classification of omicron (B.1.1.529): SARS-CoV-2 variant of concern. Nov 26, 2021. https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1....
    1. Scheepers C, Everatt J, Amoako DG, et al. The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection. medRxiv. 2021 doi: 10.1101/2021.08.20.21262342. published online Aug 24. (preprint). - DOI
    1. National Institute for Communicable Diseases Establishing a surveillance platform to assess the clinical impact of SARS-CoV-2 variants (DATCOV-Gen) in South Africa. October, 2021. https://www.nicd.ac.za/wp-content/uploads/2021/10/NICD-Monthly-Communiqu...

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